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Virus Metagenomics in Farm Animals: A Systematic Review. Viruses 2020; 12:v12010107. [PMID: 31963174 PMCID: PMC7019290 DOI: 10.3390/v12010107] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 01/12/2020] [Accepted: 01/14/2020] [Indexed: 02/07/2023] Open
Abstract
A majority of emerging infectious diseases are of zoonotic origin. Metagenomic Next-Generation Sequencing (mNGS) has been employed to identify uncommon and novel infectious etiologies and characterize virus diversity in human, animal, and environmental samples. Here, we systematically reviewed studies that performed viral mNGS in common livestock (cattle, small ruminants, poultry, and pigs). We identified 2481 records and 120 records were ultimately included after a first and second screening. Pigs were the most frequently studied livestock and the virus diversity found in samples from poultry was the highest. Known animal viruses, zoonotic viruses, and novel viruses were reported in available literature, demonstrating the capacity of mNGS to identify both known and novel viruses. However, the coverage of metagenomic studies was patchy, with few data on the virome of small ruminants and respiratory virome of studied livestock. Essential metadata such as age of livestock and farm types were rarely mentioned in available literature, and only 10.8% of the datasets were publicly available. Developing a deeper understanding of livestock virome is crucial for detection of potential zoonotic and animal pathogens and One Health preparedness. Metagenomic studies can provide this background but only when combined with essential metadata and following the “FAIR” (Findable, Accessible, Interoperable, and Reusable) data principles.
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Strubbia S, Phan MVT, Schaeffer J, Koopmans M, Cotten M, Le Guyader FS. Characterization of Norovirus and Other Human Enteric Viruses in Sewage and Stool Samples Through Next-Generation Sequencing. FOOD AND ENVIRONMENTAL VIROLOGY 2019; 11:400-409. [PMID: 31446609 PMCID: PMC6848244 DOI: 10.1007/s12560-019-09402-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 08/17/2019] [Indexed: 05/06/2023]
Abstract
This study aimed to optimize a method to identify human enteric viruses in sewage and stool samples using random primed next-generation sequencing. We tested three methods, two employed virus enrichment based on the binding properties of the viral capsid using pig-mucin capture or by selecting viral RNA prior to library preparation through a capture using the SureSelect target enrichment. The third method was based on a non-specific biophysical precipitation with polyethylene glycol. Full genomes of a number of common human enteric viruses including norovirus, rotavirus, husavirus, enterovirus and astrovirus were obtained. In stool samples full norovirus genome were detected as well as partial enterovirus genome. A variety of norovirus sequences was detected in sewage samples, with genogroup II being more prevalent. Interestingly, the pig-mucin capture enhanced not only the recovery of norovirus and rotavirus but also recovery of astrovirus, sapovirus and husavirus. Documenting sewage virome using these methods provides information for molecular epidemiology and may be useful in developing strategies to prevent further spread of viruses.
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Affiliation(s)
- Sofia Strubbia
- Ifremer, Laboratoire de Microbiologie, LSEM-SG2M, BP 21105, 44311, Nantes Cedex 3, France
| | - My V T Phan
- Department of Viroscience, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Julien Schaeffer
- Ifremer, Laboratoire de Microbiologie, LSEM-SG2M, BP 21105, 44311, Nantes Cedex 3, France
| | - Marion Koopmans
- Department of Viroscience, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Matthew Cotten
- Department of Viroscience, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- London School of Hygiene and Tropical Medicine, London, UK
- Uganda Virus Research Institute, Entebbe, Uganda
- MRC-Centre for Virus Research, Glasgow, UK
| | - Françoise S Le Guyader
- Ifremer, Laboratoire de Microbiologie, LSEM-SG2M, BP 21105, 44311, Nantes Cedex 3, France.
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Abstract
Noroviruses are a very diverse group of viruses that infect different mammalian species. In humans, norovirus is a major cause of acute gastroenteritis. Multiple norovirus infections can occur in a lifetime as the result of limited duration of acquired immunity and cross-protection among different strains. A combination of advances in sequencing methods and improvements on surveillance has provided new insights into norovirus diversification and emergence. The generation of diverse norovirus strains has been associated with (1) point mutations on two different genes: ORF1, encoding the non-structural proteins, and ORF2, encoding the major capsid protein (VP1); and (2) recombination events that create chimeric viruses. While both mechanisms are exploited by all norovirus strains, individual genotypes utilize each mechanism differently to emerge and persist in the human population. GII.4 noroviruses (the most prevalent genotype in humans) present an accumulation of amino acid mutations on VP1 resulting in the chronological emergence of new variants. In contrast, non-GII.4 noroviruses present co-circulation of different variants over long periods with limited changes on their VP1. Notably, genetic diversity of non-GII.4 noroviruses is mostly related to the high number of recombinant strains detected in humans. While it is difficult to determine the precise mechanism of emergence of epidemic noroviruses, observations point to multiple factors that include host-virus interactions and changes on two regions of the genome (ORF1 and ORF2). Larger datasets of viral genomes are needed to facilitate comparison of epidemic strains and those circulating at low levels in the population. This will provide a better understanding of the mechanism of norovirus emergence and persistence.
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Affiliation(s)
- Gabriel I Parra
- Division of Viral Products, Food and Drug Administration, 10903 New Hampshire Avenue, Building 52/72, Room 1308, Silver Spring, MD 20993, USA
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No JS, Kim WK, Cho S, Lee SH, Kim JA, Lee D, Song DH, Gu SH, Jeong ST, Wiley MR, Palacios G, Song JW. Comparison of targeted next-generation sequencing for whole-genome sequencing of Hantaan orthohantavirus in Apodemus agrarius lung tissues. Sci Rep 2019; 9:16631. [PMID: 31719616 PMCID: PMC6851128 DOI: 10.1038/s41598-019-53043-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 10/26/2019] [Indexed: 01/06/2023] Open
Abstract
Orthohantaviruses, negative-sense single-strand tripartite RNA viruses, are a global public health threat. In humans, orthohantavirus infection causes hemorrhagic fever with renal syndrome or hantavirus cardiopulmonary syndrome. Whole-genome sequencing of the virus helps in identification and characterization of emerging or re-emerging viruses. Next-generation sequencing (NGS) is a potent method to sequence the viral genome, using molecular enrichment methods, from clinical specimens containing low virus titers. Hence, a comparative study on the target enrichment NGS methods is required for whole-genome sequencing of orthohantavirus in clinical samples. In this study, we used the sequence-independent, single-primer amplification, target capture, and amplicon NGS for whole-genome sequencing of Hantaan orthohantavirus (HTNV) from rodent specimens. We analyzed the coverage of the HTNV genome based on the viral RNA copy number, which is quantified by real-time quantitative PCR. Target capture and amplicon NGS demonstrated a high coverage rate of HTNV in Apodemus agrarius lung tissues containing up to 103–104 copies/μL of HTNV RNA. Furthermore, the amplicon NGS showed a 10-fold (102 copies/μL) higher sensitivity than the target capture NGS. This report provides useful insights into target enrichment NGS for whole-genome sequencing of orthohantaviruses without cultivating the viruses.
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Affiliation(s)
- Jin Sun No
- Department of Microbiology, College of Medicine, Korea University, Seoul, 02841, Republic of Korea
| | - Won-Keun Kim
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, 24252, Republic of Korea.,Center for Medical Science Research, College of Medicine, Hallym University, Chuncheon, 24252, Republic of Korea
| | - Seungchan Cho
- Department of Microbiology, College of Medicine, Korea University, Seoul, 02841, Republic of Korea
| | - Seung-Ho Lee
- Department of Microbiology, College of Medicine, Korea University, Seoul, 02841, Republic of Korea
| | - Jeong-Ah Kim
- Department of Microbiology, College of Medicine, Korea University, Seoul, 02841, Republic of Korea
| | - Daesang Lee
- 4th R&D Institute, Agency for Defense Development, Daejeon, 34186, Republic of Korea
| | - Dong Hyun Song
- 4th R&D Institute, Agency for Defense Development, Daejeon, 34186, Republic of Korea
| | - Se Hun Gu
- 4th R&D Institute, Agency for Defense Development, Daejeon, 34186, Republic of Korea
| | - Seong Tae Jeong
- 4th R&D Institute, Agency for Defense Development, Daejeon, 34186, Republic of Korea
| | - Michael R Wiley
- The Center for Genome Sciences, U.S. Army Medical Research Institute of Infectious Diseases at Fort Detrick, Frederick, MD, 21702, USA
| | - Gustavo Palacios
- The Center for Genome Sciences, U.S. Army Medical Research Institute of Infectious Diseases at Fort Detrick, Frederick, MD, 21702, USA
| | - Jin-Won Song
- Department of Microbiology, College of Medicine, Korea University, Seoul, 02841, Republic of Korea.
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Casto AM, Adler AL, Makhsous N, Crawford K, Qin X, Kuypers JM, Huang ML, Zerr DM, Greninger AL. Prospective, Real-time Metagenomic Sequencing During Norovirus Outbreak Reveals Discrete Transmission Clusters. Clin Infect Dis 2019; 69:941-948. [PMID: 30576430 PMCID: PMC6735836 DOI: 10.1093/cid/ciy1020] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 11/29/2018] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Norovirus outbreaks in hospital settings are a common challenge for infection prevention teams. Given the high burden of norovirus in most communities, it can be difficult to distinguish between ongoing in-hospital transmission of the virus and new introductions from the community, and it is challenging to understand the long-term impacts of outbreak-associated viruses within medical systems using traditional epidemiological approaches alone. METHODS Real-time metagenomic sequencing during an ongoing norovirus outbreak associated with a retrospective cohort study. RESULTS We describe a hospital-associated norovirus outbreak that affected 13 patients over a 27-day period in a large, tertiary, pediatric hospital. The outbreak was chronologically associated with a spike in self-reported gastrointestinal symptoms among staff. Real-time metagenomic next-generation sequencing (mNGS) of norovirus genomes demonstrated that 10 chronologically overlapping, hospital-acquired norovirus cases were partitioned into 3 discrete transmission clusters. Sequencing data also revealed close genetic relationships between some hospital-acquired and some community-acquired cases. Finally, this data was used to demonstrate chronic viral shedding by an immunocompromised, hospital-acquired case patient. An analysis of serial samples from this patient provided novel insights into the evolution of norovirus within an immunocompromised host. CONCLUSIONS This study documents one of the first applications of real-time mNGS during a hospital-associated viral outbreak. Given its demonstrated ability to detect transmission patterns within outbreaks and elucidate the long-term impacts of outbreak-associated viral strains on patients and medical systems, mNGS constitutes a powerful resource to help infection control teams understand, prevent, and respond to viral outbreaks.
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Affiliation(s)
- Amanda M Casto
- Department of Medicine, University of Washington, Seattle
| | - Amanda L Adler
- Seattle Children’s Hospital, University of Washington, Seattle
| | - Negar Makhsous
- Department of Laboratory Medicine, University of Washington, Seattle
| | | | - Xuan Qin
- Department of Medicine, University of Washington, Seattle
| | - Jane M Kuypers
- Department of Laboratory Medicine, University of Washington, Seattle
| | - Meei-Li Huang
- Department of Laboratory Medicine, University of Washington, Seattle
| | - Danielle M Zerr
- Seattle Children’s Hospital, University of Washington, Seattle
- Department of Pediatrics, University of Washington, Seattle
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Papapanagiotou EP. Foodborne Norovirus State of Affairs in the EU Rapid Alert System for Food and Feed. Vet Sci 2017; 4:E61. [PMID: 29186840 PMCID: PMC5753641 DOI: 10.3390/vetsci4040061] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 11/18/2017] [Accepted: 11/21/2017] [Indexed: 01/25/2023] Open
Abstract
The European Union Rapid Alert System for Food and Feed (EU RASFF) database is an invaluable instrument for analyzing notifications involving norovirus in food. The aim of this work was to carry out a thorough research of the alert and border rejection notifications submitted in the RASFF database from its onset until 31 August 2017. Some conclusions of interest were: (i) Denmark, France, Italy, the Netherlands and Norway have contributed the majority of alert notifications as notifying countries, (ii) France and Serbia have been cited more often in alert notifications as countries of origin, (iii) Italy and Spain have submitted the majority of border rejection notifications, (iv) Third Countries implicated more frequently in border rejection notifications for norovirus in bivalve molluscs were Vietnam and Tunisia, whereas in fruits and vegetables were China and Serbia, (v) "risk dispersion" from norovirus-contaminated food was narrow since, in just over half of all alert notifications and all of the border rejection notifications, only up to three countries were involved, and (vi) both raw (oysters and berries) and cooked (mussels) food products can present a health risk to consumers. The information retrieved from the RASFF database on norovirus-contaminated food could prove helpful in the planning of future norovirus risk analysis endeavors.
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Affiliation(s)
- Elias P Papapanagiotou
- Laboratory of Animal Food Products Hygiene-Veterinary Public Health, Department of Hygiene and Technology of Food of Animal Origin, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece.
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